5E81: 30S ribosomal protein S2

Name: PDB 5E81: Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair
Published: 2016-01-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair. Determined by X-ray diffraction at 2.95 Å resolution. Released 27 Jan 2016.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Thermus thermophilus HB8, Escherichia coli
Chains: 109
Atoms: 297,904
Mol. weight: 4556.83 kDa
Ligands: ZN, SF4, MG
Released: 27 Jan 2016

Explore 5E81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E81 contains 432 α-helices and 581 β-strands across 95 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 11: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
β-strand	18	1	11
α-helix	32-34	3
β-strand	37	1	12
β-strand	43	1	13
β-strand	49	1	13
β-strand	54	1	14
β-strand	61	1	12
α-helix	70-72	3
β-strand	77-84	8	15
β-strand	91-97	7	15
β-strand	102-106	5	15
β-strand	116-117	2	15
β-strand	130-132	3	16
α-helix	133-135	3
α-helix	137	1
β-strand	141-143	3	16
β-strand	145-146	2	17
β-strand	153-155	3	17
β-strand	163-169	7	16
β-strand	172-176	5	16
β-strand	182-186	5	16
β-strand	190-193	4	16
α-helix	199-203	5
α-helix	209-214	6
β-strand	217	1	14
α-helix	218-219	2
α-helix	223-225	3
β-strand	247	1	18
β-strand	253	1	18
α-helix	265-269	5
β-strand	270	1	16

Chain 12: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	26-30	5
β-strand	35	1	36
β-strand	40	1	36
α-helix	41-43	3
α-helix	45-47	3
α-helix	48-60	13
α-helix	78-86	9
α-helix	97-98	2
α-helix	101-108	8
α-helix	113-123	11
α-helix	132-148	17
β-strand	162-164	3	37
α-helix	171-179	9
β-strand	184-188	5	37
α-helix	194-196	3
β-strand	199-202	4	37
α-helix	208-214	7
α-helix	215-217	3

Chain 15: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13-16	4	117
β-strand	22	1	118
α-helix	23-34	12
β-strand	51-54	4	117
β-strand	61	1	118
α-helix	66-69	4
β-strand	71-75	5	119
β-strand	82-86	5	119
α-helix	87-92	6
α-helix	96-106	11
α-helix	111-118	8
β-strand	120-122	3	117
β-strand	136-137	2	117

Chain 19: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	49
β-strand	17-18	2	49
α-helix	32-34	3
β-strand	37	1	50
β-strand	54	1	51
β-strand	61	1	50
β-strand	65	1	52
α-helix	70-72	3
β-strand	77-83	7	52
β-strand	92-97	6	52
β-strand	102-106	5	52
α-helix	107-108	2
β-strand	116-117	2	52
β-strand	119	1	53
β-strand	130-132	3	53
α-helix	133-135	3
α-helix	137	1
β-strand	141-143	3	53
β-strand	145-146	2	54
β-strand	153-155	3	54
β-strand	163-169	7	53
β-strand	172-176	5	53
β-strand	182-186	5	53
β-strand	190-193	4	53
α-helix	199-203	5
α-helix	209-214	6
β-strand	217	1	51
α-helix	223-225	3
β-strand	247	1	55
β-strand	253	1	55
β-strand	270	1	53

Chain 1A: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	13-29	17
β-strand	34-38	5	123
α-helix	40-42	3
β-strand	43-49	7	124
β-strand	61-67	7	124
β-strand	71-74	4	123

Chain 1B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7

Chain 1E: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	26-31	6
β-strand	32-36	5	2
β-strand	39-42	4	2
α-helix	44-62	19
β-strand	69-71	3	3
α-helix	80-86	7
β-strand	92-93	2	3
α-helix	106-119	14
α-helix	132-149	18
β-strand	162-164	3	3
α-helix	172-179	8
β-strand	184-187	4	3
β-strand	199-201	3	3
α-helix	209-223	15

Chain 1F: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
β-strand	19	1	165
β-strand	22	1	165

86 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
16S ribosomal RNA	13, 1G	RNA	1519	Thermus thermophilus HB8
30S ribosomal protein S2	12, 1E	protein	256	Thermus thermophilus HB8	P80371 (AlphaFold model)
30S ribosomal protein S3	22, 2E	protein	239	Thermus thermophilus HB8	P80372 (AlphaFold model)
30S ribosomal protein S4	32, 3E	protein	209	Thermus thermophilus HB8	P80373 (AlphaFold model)
30S ribosomal protein S5	42, 4E	protein	162	Thermus thermophilus HB8	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	52, 5E	protein	101	Thermus thermophilus HB8	Q5SLP8
30S ribosomal protein S7	62, 6E	protein	156	Thermus thermophilus HB8	P17291
30S ribosomal protein S8	72, 7E	protein	138	Thermus thermophilus HB8	P0DOY9
30S ribosomal protein S9	82, 8E	protein	128	Thermus thermophilus HB8	P80374
30S ribosomal protein S10	1A, 1I	protein	105	Thermus thermophilus HB8	Q5SHN7
30S ribosomal protein S11	2A, 2I	protein	129	Thermus thermophilus HB8	P80376
30S ribosomal protein S12	3A, 3I	protein	132	Thermus thermophilus HB8	Q5SHN3

43 more molecules are not listed.

Sequence of entity 1 (13, 1G), FASTA

>5E81_1 16S ribosomal RNA (chains 13, 1G)
UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCA
AGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUG
GGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGA
CCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU
CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAU
GGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAA
UCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGG
GGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA
AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCC
GGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACG
GCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAA
UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC
ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACC
CGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGC
UAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUG
ACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU
ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGC
CCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCC
CGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGA
CUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC
UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCU
AAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGG
AAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACAC
ACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG
CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGU
GCGGCUGGAUCACCUCCUU

Sequence of entity 2 (12, 1E), FASTA

>5E81_2 30S ribosomal protein S2 (chains 12, 1E)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (22, 2E), FASTA

>5E81_3 30S ribosomal protein S3 (chains 22, 2E)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (32, 3E), FASTA

>5E81_4 30S ribosomal protein S4 (chains 32, 3E)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (42, 4E), FASTA

>5E81_5 30S ribosomal protein S5 (chains 42, 4E)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (52, 5E), FASTA

>5E81_6 30S ribosomal protein S6 (chains 52, 5E)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (62, 6E), FASTA

>5E81_7 30S ribosomal protein S7 (chains 62, 6E)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (72, 7E), FASTA

>5E81_8 30S ribosomal protein S8 (chains 72, 7E)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (82, 8E), FASTA

>5E81_9 30S ribosomal protein S9 (chains 82, 8E)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (1A, 1I), FASTA

>5E81_10 30S ribosomal protein S10 (chains 1A, 1I)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (2A, 2I), FASTA

>5E81_11 30S ribosomal protein S11 (chains 2A, 2I)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (3A, 3I), FASTA

>5E81_12 30S ribosomal protein S12 (chains 3A, 3I)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
SF4	Iron/sulfur cluster	Fe4 S4	2
MG	Magnesium ion	Mg	1403

Primary citation

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Rozov, A., Demeshkina, N., Khusainov, I. et al. Nat Commun (2016) 7:10457-10457. DOI 10.1038/ncomms10457 · PubMed

Other PDB entries of the same protein (UniProt P80371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…

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